Phriction Projects Wikis Bioimaging And Optics Platform Image Processing OMERO EPFL OMERO account creation History Version 15 vs 19
Version 15 vs 19
Version 15 vs 19
Content Changes
Content Changes
= OMERO account creation =
The EPFL OMERO server can be accessed at [[ https://omero.epfl.ch/ | https://omero.epfl.ch/ ]].
(NOTE) As an EPFL member, you can connect to the EPFL OMERO server by entering your gaspar credentials. Your OMERO account is automatically created at first connection.
{F16653820, height=300}
= OMERO groups and EPFL units =
As soon as your OMERO account is created, you will be affiliated to the OMERO group that correspond to your default EPFL accreditation.
You can find your default accreditation by typing your name at [[ https://people.epfl.ch/ | https://people.epfl.ch/ ]]: The EPFL unit that is displayed on top corresponds to your default accreditation.
In OMERO.web, you can see your groups in the up-left corner of the web interface, next to your name and below the OMERO logo:
{F17940342, float}
Please contact [[mailto:claire.stoffel@epfl.ch | Claire Stoffel]] if you do not belong to the right OMERO group (e.g you're in a doctoral school group instead of a lab group).
= Group owners =
Your group may have **one or more owners**. The group owner has some additional rights compared to a standard group member, including : adding other members to the group, importing data for another member, and changing data's ownership.
(IMPORTANT) Please contact [[mailto:claire.stoffel@epfl.ch | Claire Stoffel]] if you want to become the owner of your OMERO group. It will allow you to manage the group yourself.
As soon as you own a group, here is how you can:
- Add new members to the group you own
Clic on your name in the top-right corner, and select {nav User settings}
{F20210625}
Go under {nav My groups} and hit the {nav Edit} button on the group you want to edit (you can own multiple groups)
{F20210642, width=400}
From the {nav Members} field, browse the OMERO user list or start typing a name. Select the user(s) you want to add and hit {nav Save}
{F20210662, width=400}
- Import data for other members
This is explained in the [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/data-upload/ | Importing (and downloading) images]] page, under **Import images**
- Change data's ownership
From the left-hand tree in OMERO.web, right clic on a container (project or dataset) or on an image, and select {nav Change Owner...}
{F20210675}
Select the new data owner from the list.
= Group permissions =
There are four different permission levels in OMERO.
{F17940637, size=full}
**By default, OMERO groups are private. To collaborate with other members from your lab, this default permission needs to be modified. Please contact [[mailto:claire.stoffel@epfl.ch | Claire Stoffel]] if you want to change the permission of an OMERO group you belong to.**
- **Private**
This group is the most restrictive:
A private Group owner can see and control who the group members are and can view their data.
As a Group member, you will only ever be able to see your own data.
(NOTE) This can be used for general data storage, access and analysis, but has very limited collaboration potential other than for the Group owner to see other group members’ data.
- **Read-only**
This group allows visibility of other users and their data, but minimal ability to annotate their data:
The Group owner can control group members as above and can perform annotations on the other group members data.
Group member can see who other members are and view their data, but cannot annotate another members’ data at all.
(NOTE) Scientists submitting a publication could move data to a read-only group as part of the publication workflow, making them publicly available via a URL for reviewers and readers (see the Help guide for [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/publish/ | publishing data using OMERO.web ]]).
- **Read-annotate**
This group permission allows some collaboration on other members’ data for all members:
Group member can view other members, their data and can make annotations on those other members’ data.
- **Read-write**
This group essentially allows all the group members to behave as if they co-own all the data:
Group member can view, annotate, edit and delete all data; the only restriction is that they cannot move other members’ data into another group.
---
{icon hand-o-right} [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/data-upload/ | NEXT STEP: Importing Data ]]
---
https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/GroupsAndPermissions
= OMERO account creation =
The EPFL OMERO server can be accessed at [[ https://omero.epfl.ch/ | https://omero.epfl.ch/ ]].
(NOTE) As an EPFL member, you can connect to the EPFL OMERO server by entering your gaspar credentials. Your OMERO account is automatically created at first connection.
{F16653820, height=300}
= OMERO groups and EPFL units =
As soon as your OMERO account is created, you will be affiliated to the OMERO group that correspond to your default EPFL accreditation.
You can find your default accreditation by typing your name at [[ https://people.epfl.ch/ | https://people.epfl.ch/ ]]: The EPFL unit that is displayed on top corresponds to your default accreditation.
In OMERO.web, you can see your groups in the up-left corner of the web interface, next to your name and below the OMERO logo:
{F17940342, float}
Please contact [[mailto:claire.stoffel@epfl.ch | Claire Stoffel]] if you do not belong to the right OMERO group (e.g you're in a doctoral school group instead of a lab group).
= Group owners =
Your group may have **one or more owners**. The group owner has some additional rights compared to a standard group member, including : adding other members to the group, importing data for another member, and changing data's ownership.
(IMPORTANT) Please contact [[mailto:claire.stoffel@epfl.ch | Claire Stoffel]] if you want to become the owner of your OMERO group. It will allow you to manage the group yourself.
As soon as you own a group, here is how you can:
- Add new members to the group you own
Clic on your name in the top-right corner, and select {nav User settings}
{F20210625}
Go under {nav My groups} and hit the {nav Edit} button on the group you want to edit (you can own multiple groups)
{F20210642, width=400}
From the {nav Members} field, browse the OMERO user list or start typing a name. Select the user(s) you want to add and hit {nav Save}
{F20210662, width=400}
- Import data for other members
This is explained in the [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/data-upload/ | Importing (and downloading) images]] page, under **Import images**
- Change data's ownership
From the left-hand tree in OMERO.web, right clic on a container (project or dataset) or on an image, and select {nav Change Owner...}
{F20210675}
Select the new data owner from the list.
= Group permissions =
There are four different permission levels in OMERO.
{F17940637, size=full}
**By default, OMERO groups are private. To collaborate with other members from your lab, this default permission needs to be modified. Please contact [[mailto:claire.stoffel@epfl.ch | Claire Stoffel]] if you want to change the permission of an OMERO group you belong to.**
- **Private**
This group is the most restrictive:
A private Group owner can see and control who the group members are and can view their data.
As a Group member, you will only ever be able to see your own data.
(NOTE) This can be used for general data storage, access and analysis, but has very limited collaboration potential other than for the Group owner to see other group members’ data.
- **Read-only**
This group allows visibility of other users and their data, but minimal ability to annotate their data:
The Group owner can control group members as above and can perform annotations on the other group members data.
Group member can see who other members are and view their data, but cannot annotate another members’ data at all.
(NOTE) Scientists submitting a publication could move data to a read-only group as part of the publication workflow, making them publicly available via a URL for reviewers and readers (see the Help guide for [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/publish/ | publishing data using OMERO.web ]]).
- **Read-annotate**
This group permission allows some collaboration on other members’ data for all members:
Group member can view other members, their data and can make annotations on those other members’ data.
- **Read-write**
This group essentially allows all the group members to behave as if they co-own all the data:
Group member can view, annotate, edit and delete all data; the only restriction is that they cannot move other members’ data into another group.
---
{icon hand-o-right} [[ https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/omero/data-upload/ | NEXT STEP: Importing Data ]]
---https://wiki-biop.epfl.ch/en/Image_Storage/OMERO/GroupsAndPermissions
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